This report is recent as of 2021-01-06 12:08 GMT. All SARS-CoV-2 sequences were downloaded from GISAID and genomes were de-duplicated based on GISAID sequence name – note that the publically available metadata may not fully allow us to de-duplicate by patient. Full data processing pipeline found here.
The sequences were then assigned lineages with pangolin v2.1.6, pangoLEARN version 2020-12-17-2.
Pangolin assigns B.1.1.7 to sequences with more than 4 of the 17 defining B.1.1.7 SNPs – defined here
| Lineage | Country count | Country | Sequence count | Earliest sequence | Travel history |
|---|---|---|---|---|---|
| B.1.1.7 | 28 | UK 7711, Denmark 76, Portugal 35, Italy 24, Finland 14, France 14, Netherlands 13, Australia 10, Sweden 9, USA 9, Singapore 7, Ireland 7, Switzerland 6, New_Zealand 6, Germany 5, Spain 4, Jamaica 4, Israel 4, South_Korea 3, India 3, Luxembourg 3, Hong_Kong 3, Norway 2, Brazil 2, Pakistan 2, Canada 1, Oman 1, Lebanon 1 | 7979 | 2020-09-20 |
Caveat: Most locations outside the original focus have not reported sustained transmission and many cases have known travel links to the focal location. Increasing numbers of international cases is currently likely due to increased surveillance and vigilance.
| Statistic | Information |
|---|---|
| Sequence count | 7979 |
| Countries with sequences | 28 |
| Countries reported | 45 |
| Likely origin | United Kingdom |
| SNPs | aa:orf1ab:T1001I aa:orf1ab:A1708D aa:orf1ab:I2230T del:11288:9 del:21765:6 del:21991:3 aa:S:N501Y aa:S:A570D aa:S:P681H aa:S:T716I aa:S:S982A aa:S:D1118H aa:Orf8:Q27* aa:Orf8:R52I aa:Orf8:Y73C aa:N:D3L aa:N:S235F |
The number of ticketed origin-to-destination journeys from London airports to countries outside the United Kingdom during October 2020.
Colours indicate numbers of published genomes of B.1.1.7 deposited on GISAID. Grey bars indicate countries that have reported the presence of the variant but have not yet published B.1.1.7 sequences on GISAID. White bars indicate countries with no reports of B.1.1.7.
Flight data come from the International Air Transportation Association that capture anonymized, passenger-level flight itinerary data, comprising both commercial flights and scheduled charter flights. These data account for ~90% of global air travel volumes, with the remaining volumes modelled using market intelligence. We report data from destinations including >5,000 passengers.
Note that flight data reflects final-destination on a booked journey, we cannot account for instances where two separate tickets were purchased.
Data from Kamran Khan, Isaac Bogoch, Alexander Watts, Oliver Pybus, Moritz Kraemer
Country count: 45